Le récepteur minéralocorticoïde (MR), activé par l’aldostérone, exerce de nombreuses fonctions pléïotropes, notamment au niveau rénal où il régule l’homéostasie hydrosodée. Des dysfonctionnements de la signalisation minéralocorticoïde sont impliqués dans des pathologies majeures chez l’Homme. Dans ce travail, nous avons identifié par ChIP sequencing le premier cistrome du MR dans une lignée cellulaire rénale humaine. La caractérisation des cibles génomiques a permis de décrire l’élément de réponse spécifique du MR, et de démontrer l’existence de deux modes d’action pour le MR : par liaison directe à l’ADN, ou indirecte via la liaison à d’autres facteurs de transcription. Le MR est physiologiquement confronté à une dualité face au récepteur glucocorticoïde (GR) avec lequel il partage un ligand, le cortisol, et des cibles génomiques, dont le gène PER1. Sur ce dernier, les deux récepteurs se distinguent par des recrutements dynamiques et cycliques différents, variants selon l’hormone, et contemporains de celui de partenaires transcriptionnels, régulant ainsi des effets à court ou à long-terme. Enfin, par ChIP en série et en tandem, nous avons montré que le MR et le GR agissent sous forme d’homodimères ou d’hétérodimères.L’identification du cistrome du MR, et la caractérisation de ses mécanismes d’action moléculaires, améliore notre compréhension de la physiopathologie de la signalisation minéralocorticoïde, et pourrait aboutir, notamment par le développement d’antagonistes sélectifs du MR comme la Finérénone, à de nouvelles stratégies thérapeutiques. / The mineralocorticoid receptor (MR), activated by aldosterone, exhibits numerous pleiotropic functions, most notably at the renal level where it regulates electrolytic homeostasis. Dysfunctions in the mineralocorticoid signaling pathway are involved in major diseases in Human. During this work, we have identified by ChIP sequencing the first MR cistrome in a human renal cell lineage. The characterization of the identified genomic targets allowed us to define a specific MR responsive element, and to demonstrate the existence of two transactivation processes for MR: through direct binding to DNA or through indirect interaction via binding to other transcription factors. MR is physiologically confronted with a duality with the glucocorticoid receptor (GR), since they share a common ligand, cortisol, and some of their genomic targets, whose PER1 gene. On the latter, MR and GR are distinguished by different dynamic and cyclical recruitment, varying according to hormone, and coordinated with the one of transcriptional partners, translating into the regulation of short-term and long-term effects. Finally, by serial and tandem ChIP experiment, we have demonstrated that MR and GR act as homodimer and as heterodimer.Identification of new MR genomic targets and characterization of its molecular mechanisms of action, improve our understanding of the pathophysiology of the mineralocorticoid signaling pathway. This could ultimately, notably through the development of selective MR antagonists like Finerenone, lead to new therapeutic strategies.

No description available.

Psychiatric disorders are believed to result from the combination of genetic predisposition and many environmental triggers. While the large number of disease-associated genetic variations have been recognized by previous genome-wide association studies (GWAS), the role of epigenetic mechanisms that mediate the effects of environmental factors on CNS gene activity in the etiology of most mental illnesses is still largely unclear. A growing body of evidence suggested that the abnormalities (changes in gene expression, formation of neural circuits, and behavior) involved in most psychiatric syndromes are preserved by epigenetic modifications identified in several specific brain regions. In this thesis, we developed the second generation of one of our microfluidic technologies (MOWChIP-seq) and used it to profile genome-wide histone modifications in three mental illness-related biological studies: the effect of psychedelics in mice, schizophrenia, and the effect of maternal immune activation in mice offspring. The second generation of MOWChIP-seq was designed to generate histone modification profiles from as few as 100 cells per assay with a throughput as high as eight assays in each run. Then, we applied the new MOWChIP-seq and SMART-seq2 to profile the histone modification H3K27ac and transcriptome, respectively, using NeuN+ neuronal nuclei from the mouse frontal cortex after a single dose of psychedelic administration. The epigenomic and transcriptomic changes induced by 2,5-Dimethoxy-4-iodoamphetamine (DOI), a subtype of psychedelics, in mouse neuronal nuclei at various time points suggest that the long-lasting effects of the psychedelic are more closely related to epigenomic alterations than the changes in transcriptomic patterns. Next, we comprehensively characterized epigenomic and transcriptomic features from the frontal cortex of 29 individuals with schizophrenia and 29 individually matched controls (gender and age). We found that schizophrenia subjects exhibited thousands of neuronal vs. glial epigenetic differences at regions that included several susceptibility genetic loci, such as NRXN1, RGS4 and GRIN3A. Finally, we investigated the epigenetic and transcriptomic alterations induced by the maternal immune activation (MIA) in mice offspring's frontal cortex. Pregnant mice were injected with influenza virus at GD 9.5 and the frontal cortex from mice pups (10 weeks old) were examined later. The results offered us some insights into the contribution of MIA to the etiology of some mental disorders, like schizophrenia and autism. / Doctor of Philosophy / While this field is still in its early stage, the epigenetic studies of mental disorders present promise to expand our understanding about how environmental stimulates, interacting with genetic factors, contribute to the etiology of various psychiatric syndromes, like major depression and schizophrenia. Previous clinical trials suggested that psychedelics may represent a promising long-lasting treatment for patients with depression and other psychiatric conditions. These research presented the therapeutic potential of psychedelic compounds for treating major depression and demonstrated the capability of psychedelics in increasing dendritic density and stimulating synapse formation. However, the molecular mechanism mediating the clinical effectiveness of psychedelics remain largely unexplored. Our study revealed that epigenomic-driven changes in synaptic plasticity sustain psychedelics' long-lasting antidepressant action. Another serious mental illness is schizophrenia, which could affect how an individual feels, thinks, and behaves. Like most other mental disorders, schizophrenia results from a combination of genetic and environmental causes. Epigenetic marks allow a dynamic impact of environmental factors, including antipsychotic medications, on the access to genes and regulatory elements. Despite this, no study so far has profiled cell-type-specific genome-wide histone modifications in postmortem brain samples from schizophrenia subjects or the effect of antipsychotic treatment on such epigenetic marks. Here we show the first comprehensive epigenomic characterization of the frontal cortex of 29 individuals with schizophrenia and 29 matched controls. The process of brain development is surprisingly sensitive to a lot of environmental insults. Epidemiological studies have recognized maternal immune activation as a risk factor that may change the normal developmental trajectory of the fetal brain and increase the odds of developing a range of psychiatric disorders, including schizophrenia and autism, in its lifetime. Given the prevalence of the coronavirus, uncovering the molecular mechanism underlie the phenotypic alterations has become more urgent than before, for both prevention and treatment.

Epigenetic modifications, such as DNA methylation and histone modifications, play important roles in gene expression and regulation, and are highly involved in cellular processes such as stem cell pluripotency/differentiation and tumorigenesis. Chromatin immunoprecipitation (ChIP) is the technique of choice for examining in vivo DNA-protein interactions and has been a great tool for studying epigenetic mechanisms. However, conventional ChIP assays require millions of cells for tests and are not practical for examination of samples from lab animals and patients. Automated microfluidic chips offer the advantage to handle small sample sizes and facilitate rapid reaction. They also eliminate cumbersome manual handling. In this report, I will talk about three different projects that utilized microfluidic immunoprecipitation followed by next genereation sequencing technologies to enable low input and high through epigenomics profiling. First, I examined RNA polymerase II transcriptional regulation with microfluidic chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) assays. Second, I probed the temporal dynamics in the DNA methylome during cancer development using a transgenic mouse model with microfluidic methylated DNA immunoprecipitation followed by next generation sequencing (MeDIP-seq) assays. Third, I explored negative enrichment of circulating tumor cells (CTCs) followed by microfluidic ChIP-seq technology for studying temporal dynamic histone modification (H3K4me3) of patient-derived tumor xenograft on an immunodeficient mouse model during the course of cancer metastasis. In the first study, I adapted microfluidic ChIP-seq devices to achieve ultrahigh sensitivity to study Pol2 transcriptional regulation from scarce cell samples. I dramatically increased the assay sensitivity to an unprecedented level (~50 K cells for pol2 ChIP-seq). Importantly, this is three orders of magnitude more sensitive than the prevailing pol2 ChIP-seq assays. I showed that MNase digestion provided better ChIP-seq signal than sonication, and two-steps fixation with MNase digestion provided the best ChIP-seq quality followed by one-step fixation with MNase digestion, and lastly, no fixation with MNase digestion. In the second study, I probed dynamic epigenomic changes during tumorigenesis using mice often require profiling epigenomes using a tiny quantity of tissue samples. Conventional epigenomic tests do not support such analysis due to the large amount of materials required by these assays. In this study, I developed an ultrasensitive microfluidics-based methylated DNA immunoprecipitation followed by next-generation sequencing (MeDIP-seq) technology for profiling methylomes using as little as 0.5 ng DNA (or ~100 cells) with 1.5 h on-chip process for immunoprecipitation. This technology enabled me to examine genome-wide DNA methylation in a C3(1)/SV40 T-antigen transgenic mouse model during different stages of mammary cancer development. Using this data, I identified differentially methylated regions and their associated genes in different periods of cancer development. Interestingly, the results showed that methylomic features are dynamic and change with tumor developmental stage. In the last study, I developed a negative enrichment of CTCs followed by ultrasensitive microfluidic ChIP-seq technology for profiling histone modification (H3K4Me3) of CTCs to resolve the technical challenges associated with CTC isolation and difficulties related with tools for profiling whole genome histone modification on tiny cell samples. / Ph. D. / The human genome has been sequenced and completed over a decade ago. The information provided by the genomic map inspired numerous studies on genetic variations and their roles in diseases. However, genomic information alone is not always sufficient to explain important biological processes. Gene activation and expression are not only associated with alteration in the DNA sequence, but also affected by other changes to DNA and histones. Epigenetics refers to the molecular mechanisms that affect gene expression and phenotypes without involving changes in the DNA sequence. For example, the DNA can get methylated, the histone protein that is wrapped around by DNA can also get methylated or acetylatied, and transcription factors can bind to different part of DNA. All of these can affect gene expression without alter the DNA sequences. Epigenetic changes occur throughout all stages of cell development or in response to environmental cues. They change transcription patterns in a tissue/cell-specific fashion. For example, transcriptional silencing of tumor-suppressor genes by DNA methylation plays an important role in cancer development. Therefore, understanding of epigenetic regulations will help to improve various aspects of biomedicine. For instance, personalized medicine can be vi tailored based on epigenetic profile of certain patient to specifically control gene expression in the disease treatment. However, the technology for profiling epigenetic modifications, i.e. Chromatin Immunoprecipitation (ChIP), suffers from serious limitations. The key limitation is the sensitivity of the assay. Conventional assay requires a large number of cells (>10⁶ cells per ChIP). This is feasible when using cell lines. However, such requirement has become a major challenge when primary cells are used because very limited amounts of samples can be generated from lab animals or patients. Population heterogeneity information may also be lost when a large cell number is used. In this project, we developed an automated ultrasensitive microfluidic chromatin/DNA immunoprecipitation followed by next-generation sequencing (ChIP/MeDIP-Seq) technology for profiling epigenetic modifications (e.g., histone modifications, transcriptional regulations, and DNA methylation). We extensively optimized design parameters for each and every step of ChIP/MeDIP (e.g. sonication/crosslinking time, antibody concentration, washing conditions) in order to reach highest sensitivity of 0.1 ng DNA (or ~50-100 cells) as starting material for IP, which is roughly 4-5 orders of magnitude higher than the prevailing protocol and 2-3 orders of magnitude higher than the-state-of-the-art(~50 ng). With such sensitivity, we were able to study temporal dynamics in the DNA methylomes during the various stages of mammary cancer development from a transgenic mouse mode. We were able to investigate transcriptional regulation of RNA polymerase II from scarce cell samples. We were also able to study histone modification (H3K4Me3) of circulating tumor cells during cancer metastasis.

La chromatine est plus qu’un système d’empaquetage de l’ADN ; elle est le support de toutes les réactions liées à l’ADN dans le noyau des cellules eucaryotes et participe au contrôle de l’accès de l’ARN polymérase II (ARNPolII) à l’ADN. Responsable de la transcription de tous les ARNm des cellules eucaryotes, l’ARNPolII doit, suivant son recrutement aux promoteurs des gènes, transcrire l’ADN en traversant la matrice chromatinienne. Grâce au domaine C-terminal (CTD) de sa sous-unité Rpb1, elle coordonne la maturation de l’ARNm en cours de synthèse ainsi que les modifications de la chromatine, concomitantes à la transcription. Cette thèse s’intéresse à deux aspects de la transcription : la matrice, avec la localisation de la variante d’histone H2A.Z, et la machinerie de transcription avec le cycle de phosphorylation du CTD de l’ARNPolII. Suivant l’introduction, le chapitre 2 de cette thèse constitue un protocole détaillé et annoté de la technique de ChIP-chip, chez la levure Saccharomyces cerevisiae. Cette technique phare dans l’étude in vivo des phénomènes liés à l’ADN a grandement facilité l’étude du rôle de la chromatine dans les phénomènes nucléaires, en permettant de localiser sur le génome les marques et les variantes d’histones. Ce chapitre souligne l’importance de contrôles adéquats, spécifiques à l’étude de la chromatine. Au chapitre 3, grâce à la méthode de ChIP-chip, la variante d’histone H2A.Z est cartographiée au génome de la levure Saccharomyces cerevisiae avec une résolution d’environ 300 paires de bases. Nos résultats montrent que H2A.Z orne un à deux nucléosomes au promoteur de la majorité des gènes. L’enrichissement de H2A.Z est anticorrélé à la transcription et nos résultats suggèrent qu’elle prépare la chromatine pour l’activation des gènes. De plus H2A.Z semble réguler la localisation des nucléosomes. Le chapitre suivant s’intéresse à la transcription sous l’angle de la machinerie de transcription en se focalisant sur le cycle de phosphorylation de l’ARN polymérase II. Le domaine C-terminal de sa plus large sous-unité est formé de répétitions d’un heptapeptide YSPTSPS dont les résidus peuvent être modifiés au cours de la transcription. Cette étude localise les marques de phosphorylation des trois résidus sérine de manière systématique dans des souches mutantes des kinases et phosphatases. Nos travaux confirment le profil universel des marques de phosphorylations aux gènes transcrits. Appuyés par des essais in vitro, ils révèlent l’interaction complexe des enzymes impliqués dans la phosphorylation, et identifient Ssu72 comme la phosphatase de la sérine 7. Cet article appuie également la notion de « variantes » des marques de phosphorylation bien que leur étude spécifique s’avère encore difficile. La discussion fait le point sur les travaux qui ont suivi ces articles, et sur les expériences excitantes en cours dans notre laboratoire. / Chromatin is more than just the eucaryotic DNA packaging system; it is the substrate of all reactions involving DNA in eukaryotic cells and actively regulates RNA Polymerase II (RNAPolII) access to DNA. Responsible for all mRNA transcription in eucaryotes, the RNAPolII must, following its recruitment to the pre-initiation complex, overcome the chromatin barrier in order to transcribe genes. The RNAPolII CTD allows for the co-transcriptional coordination of mRNA maturation and chromatin modifications. The work covered in this thesis addresses two aspects of transcription: the chromatin substrate, with the localization of H2A variant, H2A.Z, and the transcription complex with the phosphorylation cycle of the RNAPolII CTD. Following the introduction, chapter 2 constitutes a detailed and annotated Saccharomyces cerevisiae ChIP-chip protocol, from the culture to the hybridization of the array, with an emphasis on the proper controls required for chromatin study. This technique, extremely powerful for the in vivo study of all DNA transactions, leads to a better understanding of chromatin function in nuclear phenomena, thanks to the localization of histone variants and modifications. The third chapter maps the H2A.Z variant across the yeast genome at ~300 base pairs resolution using ChIP-chip. Our data shows that H2A.Z is incorporated into one or two promoter-bound nucleosomes at the majority of genes. H2A.Z enrichment is anticorrelated with transcription, and the results suggest that it configures chromatin structure to poise genes for transcriptional activation. Furthermore, we have shown that H2A.Z can regulate nucleosome positioning. The next chapter focuses on the transcription machinery and, more precisely, on the phosphorylation cycle of RNAPolII. The CTD contains repetitions of a heptapeptide (YSPTSPS) on which all serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Here, we systematically profiled the location of the RNAPII phospho-isoforms in wild-type cells and mutants for most CTD modifying enzymes. The results provide evidence for a uniform CTD cycle across genes. Together with results from in vitro assays, these data reveal a complex interplay between the modifying enzymes, identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes. Moreover, it reinforces the notion of variants of the phosphorylation marks, even though the exact nature of the variant is still difficult to identify. The discussion introduces the studies that followed this work, including new projects conceived in our lab.

La chromatine est plus qu’un système d’empaquetage de l’ADN ; elle est le support de toutes les réactions liées à l’ADN dans le noyau des cellules eucaryotes et participe au contrôle de l’accès de l’ARN polymérase II (ARNPolII) à l’ADN. Responsable de la transcription de tous les ARNm des cellules eucaryotes, l’ARNPolII doit, suivant son recrutement aux promoteurs des gènes, transcrire l’ADN en traversant la matrice chromatinienne. Grâce au domaine C-terminal (CTD) de sa sous-unité Rpb1, elle coordonne la maturation de l’ARNm en cours de synthèse ainsi que les modifications de la chromatine, concomitantes à la transcription. Cette thèse s’intéresse à deux aspects de la transcription : la matrice, avec la localisation de la variante d’histone H2A.Z, et la machinerie de transcription avec le cycle de phosphorylation du CTD de l’ARNPolII. Suivant l’introduction, le chapitre 2 de cette thèse constitue un protocole détaillé et annoté de la technique de ChIP-chip, chez la levure Saccharomyces cerevisiae. Cette technique phare dans l’étude in vivo des phénomènes liés à l’ADN a grandement facilité l’étude du rôle de la chromatine dans les phénomènes nucléaires, en permettant de localiser sur le génome les marques et les variantes d’histones. Ce chapitre souligne l’importance de contrôles adéquats, spécifiques à l’étude de la chromatine. Au chapitre 3, grâce à la méthode de ChIP-chip, la variante d’histone H2A.Z est cartographiée au génome de la levure Saccharomyces cerevisiae avec une résolution d’environ 300 paires de bases. Nos résultats montrent que H2A.Z orne un à deux nucléosomes au promoteur de la majorité des gènes. L’enrichissement de H2A.Z est anticorrélé à la transcription et nos résultats suggèrent qu’elle prépare la chromatine pour l’activation des gènes. De plus H2A.Z semble réguler la localisation des nucléosomes. Le chapitre suivant s’intéresse à la transcription sous l’angle de la machinerie de transcription en se focalisant sur le cycle de phosphorylation de l’ARN polymérase II. Le domaine C-terminal de sa plus large sous-unité est formé de répétitions d’un heptapeptide YSPTSPS dont les résidus peuvent être modifiés au cours de la transcription. Cette étude localise les marques de phosphorylation des trois résidus sérine de manière systématique dans des souches mutantes des kinases et phosphatases. Nos travaux confirment le profil universel des marques de phosphorylations aux gènes transcrits. Appuyés par des essais in vitro, ils révèlent l’interaction complexe des enzymes impliqués dans la phosphorylation, et identifient Ssu72 comme la phosphatase de la sérine 7. Cet article appuie également la notion de « variantes » des marques de phosphorylation bien que leur étude spécifique s’avère encore difficile. La discussion fait le point sur les travaux qui ont suivi ces articles, et sur les expériences excitantes en cours dans notre laboratoire. / Chromatin is more than just the eucaryotic DNA packaging system; it is the substrate of all reactions involving DNA in eukaryotic cells and actively regulates RNA Polymerase II (RNAPolII) access to DNA. Responsible for all mRNA transcription in eucaryotes, the RNAPolII must, following its recruitment to the pre-initiation complex, overcome the chromatin barrier in order to transcribe genes. The RNAPolII CTD allows for the co-transcriptional coordination of mRNA maturation and chromatin modifications. The work covered in this thesis addresses two aspects of transcription: the chromatin substrate, with the localization of H2A variant, H2A.Z, and the transcription complex with the phosphorylation cycle of the RNAPolII CTD. Following the introduction, chapter 2 constitutes a detailed and annotated Saccharomyces cerevisiae ChIP-chip protocol, from the culture to the hybridization of the array, with an emphasis on the proper controls required for chromatin study. This technique, extremely powerful for the in vivo study of all DNA transactions, leads to a better understanding of chromatin function in nuclear phenomena, thanks to the localization of histone variants and modifications. The third chapter maps the H2A.Z variant across the yeast genome at ~300 base pairs resolution using ChIP-chip. Our data shows that H2A.Z is incorporated into one or two promoter-bound nucleosomes at the majority of genes. H2A.Z enrichment is anticorrelated with transcription, and the results suggest that it configures chromatin structure to poise genes for transcriptional activation. Furthermore, we have shown that H2A.Z can regulate nucleosome positioning. The next chapter focuses on the transcription machinery and, more precisely, on the phosphorylation cycle of RNAPolII. The CTD contains repetitions of a heptapeptide (YSPTSPS) on which all serines are differentially phosphorylated along genes in a prescribed pattern during the transcription cycle. Here, we systematically profiled the location of the RNAPII phospho-isoforms in wild-type cells and mutants for most CTD modifying enzymes. The results provide evidence for a uniform CTD cycle across genes. Together with results from in vitro assays, these data reveal a complex interplay between the modifying enzymes, identify Ssu72 as the Ser7 phosphatase and show that proline isomerization is a key regulator of CTD dephosphorylation at the end of genes. Moreover, it reinforces the notion of variants of the phosphorylation marks, even though the exact nature of the variant is still difficult to identify. The discussion introduces the studies that followed this work, including new projects conceived in our lab.

Huntington’s disease (HD) is a neurodegenerative disorder caused by the inheritance of one mutant copy of the huntingtin gene. Mutant huntingtin protein (mHtt) contains an expanded polyglutamine repeat region near the N-terminus. Cleavage of mHtt releases an N-terminal fragment (N-mHtt) which translocates, and accumulates in the nucleus. Nuclear accumulation of N-mHtt has been directly associated with cellular toxicity. Decreased transcription is among the earliest detected changes that occur in the brains of HD patients and is consistently observed in all animal and cellular models of HD. Transcriptional dysregulation may trigger many of the perturbations that occur later in disease progression and an understanding of the effects of mHtt may lead to strategies to slow the progression of the disease. Current models of N-mHtt-mediated transcriptional dysregulation suggest that abnormal interactions between N-mHtt and transcription factors impair the ability of these transcription factors to associate at N-mHtt-affected promoters and properly regulate gene expression. We tested various aspects of these models using two N-mHtt-affected promoters in in vitro transcription assays and in two cell models of HD using techniques including overexpression of known N-mHtt-interacting transcription factors, chromatin immunoprecipitation, promoter deletion and mutation analyses and in vitro promoter binding assays. Based on our results and those in the literature, we proposed a new model of N-mHtt-mediated transcriptional dysregulation centered on the presence of N-mHtt at affected promoters. We concluded that simultaneous interaction of N-mHtt with multiple binding partners within the transcriptional machinery would explain the gene-specificity of N-mHtt-mediated transcriptional dysregulation, as well as the observation that some genes are affected early in disease progression while others are affected later. Our model explains why alleviating N-mHtt-mediated transcriptional dysregulation through overexpression of N-mHtt-interacting proteins has proven to be difficult and suggests that the most realistic strategy for restoring gene expression across the spectrum of N-mHtt affected genes is by reducing the amount of soluble nuclear N-mHtt.

Dissertation (Ph.D.)--University of South Florida, 2007. / Title from PDF of title page. Document formatted into pages; contains 82 pages. Includes vita. Includes bibliographical references.

Abstract Wnt genes encode secreted signalling molecules that control embryonic development including organogenesis, while dysregulated Wnt signalling is connected to many diseases such as cancer. Specifically, Wnts control a number of cellular processes such as proliferation, adhesion, differentiation and aging. Many Wnt proteins activate the canonical β-catenin signalling pathway that regulates transcription of a still poorly characterized set of target genes. Wnts also transduce their signaling in cells via β-catenin-independent “non-canonical” pathways, which are not well understood. In this study, Wnt-11 signalling mechanisms in a mammalian model cell line and roles of Wnt-11 in heart development were analyzed in detail. In addition the aim was to identify new Wnt target genes by direct chromatin immunoprecipitation and Affymetrix GeneChip assays in the model cells exposed to Wnt-3a. Our studies reveal that Wnt-11 signalling coordinates the activity of key cell signalling pathways, namely the canonical Wnt/β-catenin, the JNK/AP-1, the NF-κB and PI3K/Akt pathways in the CHO cells. Analysis of the Wnt-11-deficient embryos revealed a crucial role in heart organogenesis. Wnt-11 signalling coordinates cell interactions during assembly of the myocardial wall and Wnt-11 localizes the expression of N-cadherin and β-catenin to specific cellular domains in the embryonic ventricular cardiomyocytes. Collectively these studies reveal that the mammalian Wnt-11 behaves as a non-canonical Wnt and that it is a critical factor in the coordination of heart development. Specifically, it controls components of the cell adhesion machinery. Analysis of the Wnt target genes revealed a highly context-dependent profile in the Wnt-regulated genes. Several new putative target genes were discovered. Out of the candidate Wnt target genes, Disabled-2 was identified as a potential new direct target for Wnt signalling.

Microfluidics is a versatile tool with many applications in biology. Its ability to manipulate small volumes of liquid precisely has led to the development of many microfluidic assay platforms. They could handle small amounts of samples and carry out analysis with high sensitivity and throughput. Microfluidic assays have provided new insights into scarce biological samples at higher resolution. In this thesis, we developed microfluidic tools to conduct low input ChIP-seq and ChIRP-seq. We applied them to a variety of samples profiling different targets. The native MOWChIP-seq platform was developed to map RNA polymerase II, transcription factors and histone deacetylase binding in 1,000-50,000 cells. We examined mouse prefrontal cortex and cerebellum using this technology. We found extensive differences that correlated with distinct neurological functions of the brain regions. The same platform and workflow were used to profile five key histone modifications in human lung tumor and normal tissue samples. Integrative analysis with gene expression data revealed extensive chromatin remodeling in lung tumor. Spatial histone modification mapping was conducted in mouse neocortex in a similar fashion. We generated an epigenomic tomography that demonstrated the molecular state of the brain in 3D. Lastly, we developed a microfluidic version of the ChIRP-seq process which successfully conducted the assay using only 500K cells. This improvement makes ChIRP-seq in tissue samples feasible. / Doctor of Philosophy / Microfluidics is a type of technology that can control small volumes of liquid in a miniature system. It can carry out reactions on very small scales with higher precision and sensitivity than conventional methods. Microfluidics has found many uses in the field of biology, especially dealing with samples available in limited quantities. These low input microfluidic platforms have helped researchers gain new knowledge on many complex questions. In this thesis, we developed microfluidic tools to carry out low input ChIP-seq and ChIRP-seq. These are two established techniques used to map where certain targets are located on the genome of an organism. These targets include specific chemical modifications to the wrapper protein of DNA (histone modification), proteins that take part in transcription and expression of genes (RNA polymerase II, transcription factors) and other molecules. Our nMOWChIP-seq system removed the need for fixation by chemicals. It was able to examine RNA polymerase II, transcription factors and other enzymes using 1,000-50,000 cells. Traditional ChIP-seq requires more than 10 million cells and time-consuming chemical treatment steps. Our technology greatly improved sensitivity and ease of use. We also used this platform to test five important histone modifications in human lung tumors and healthy tissues. We constructed a spatial map of histone modification in mouse brain by analyzing slices of the cortex. Finally, we developed a microfluidic version of ChIRP-seq process to map locations of long non-coding RNAs in cultured human cells. The cells needed for a successful test were reduced to 500K from 20 million of the original workflow.